|
| Status |
Public on Apr 05, 2011 |
| Title |
DAF-12 TAP DAF-12 ab IP#2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
anti-DAF-12 chIP DNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: L2 Larval + Young Adult (50:50 mix)
|
| Growth protocol |
Worms were grown in liquid culture using OP50-1 as food
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
L2 larvae and adult worms were collected by floatation, briefly frozen, and then sonicated in PBS + 1% formaldehyde. Samples were fixed for a total of 30 minutes before being quenched with 0.125 M glycine.
|
| Label |
Biotin
|
| Label protocol |
DNA was amplified using the Genomeplex WGA kit from Sigma-Aldrich. The amplified DNA was labelled using the DNA terminal labeling kit from Affymetrix
|
| |
|
| Channel 2 |
| Source name |
Input genomic DNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
age: L2 Larval + Young Adult (50:50 mix)
|
| Growth protocol |
Worms were grown in liquid culture using OP50-1 as food
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
L2 larvae and adult worms were collected by floatation, briefly frozen, and then sonicated in PBS + 1% formaldehyde. Samples were fixed for a total of 30 minutes before being quenched with 0.125 M glycine.
|
| Label |
Biotin
|
| Label protocol |
DNA was amplified using the Genomeplex WGA kit from Sigma-Aldrich. The amplified DNA was labelled using the DNA terminal labeling kit from Affymetrix
|
| |
|
| |
| Hybridization protocol |
Labelled DNA was hybridized to Affymetrix GeneChip Caenorhabditis elegans Tiling 1.0R arrays at 45C overnight. Arrays were washed using a GeneChip Fluidics station from Affymetrix.
|
| Scan protocol |
Arrays were scanned using a GeneChip scanner.
|
| Description |
DAF-12 TAP IP #2
|
| Data processing |
CEL files were normalized and analyzed using TAS software from Affymetrix
BED files were generated by TAS software and have comparisons of AA86 vs input and then 3 DAF-12:TAP precipitations vs input. Genomic annotation is based on WS170 (Wormbase)
|
| |
|
| Submission date |
Apr 04, 2011 |
| Last update date |
Apr 05, 2011 |
| Contact name |
Alfred L Fisher |
| E-mail(s) |
fishera@dom.pitt.edu
|
| Phone |
412-383-5892
|
| Fax |
412-692-2370
|
| Organization name |
University of Pittsburgh
|
| Department |
Medicine
|
| Lab |
Fisher lab
|
| Street address |
3471 5th Ave., Suite 500
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15260 |
| Country |
USA |
| |
|
| Platform ID |
GPL5634 |
| Series (1) |
| GSE28350 |
Genome-wide identification of DAF-12 binding sites in Caenorhabditis elegans |
|
